This one is a list of my favorite comic book story lines. Like some other comic-book related lists of mine, this one is listed in descending order of preference.
1. The Age of Apocalypse
Written by various writers including Scott Lobdell, Mark Waid, Jeph Loeb, and Larry Hama.
This story arc took place in 1996 and was set in an alternate future where Charles Xavier (Professor X) died before he started the X-Men and the villain Apocalypse takes over North America.
2. Batman: Earth One
Written by Geoff Johns and published in 2012.
This story is a re-telling of Batman's origins.
3. Batman: Year One
Written by Frank Miller and published in 1987.
This one is Miller's interpretation of Batman's origins.
4. Kingdom Come (DC)
Written by Mark Waid and Alex Ross.
This story takes place in a distant future where most of the super heroes we know and love have retired and details their return to "duty" following a global catastrophe.
5. The Dark Knight Returns
Written by Frank Miller and published in 1986.
This story is set in a future where Batman has retired but must return to the cowl when things get out of control in Gotham.
6. The Long Halloween
Written by Jeph Loeb and published in 1996 and 1997.
This is a story set in Batman's early crime fighting days and details his hunt for the mysterious Holiday Killer.
Written by Jeph Loeb and published in 2002 and 2003.
This one tells the story of Batman on the hunt for a new serial killer that cuts the faces off his victims.
8. All Star Batman and Robin
Written by Frank Miller and published in 2005-2008.
Essentially this is a re-telling of the Boy Wonder's origins as interpreted by Frank Miller.
9. Green Lantern: Rebirth
Written by Geoff Johns and published in 2004 and 2005.
This is an origin story of Hal Jordan becoming the Green Lantern.
10. Green Arrow: Quiver
Written by Kevin Smith and published in 2001 and 2002.
This tells the story of Oliver Queen dealing with life after his resurrection from death.
11. Flash: Rebirth
Written by Geoff Johns and published in 2009 and 2010.
The one is Geoff Johns' re-telling of the Flash origin.
Written by Geoff Johns and published in 2011.
This story arc takes place in an alternate timeline caused by one of Flash's villains. The events in this story directly led to DC's New 52 re-boot.
13. Punisher: Suicide Run
Written by various writers including Chuck Dixon, Larry Hama, Mike Lackey and Steven Grant. It was published in 1992, 1993, and 1994.
This long running multiple title story arc tells the story of the events that occur after the apparent death of Frank Castle, the Punisher.
There were so many good comic book story arcs to choose from that didn't make the list, I though I'd include a list of story arcs that were really good but not quite good enough to make the "13" cut. These are not listed in any particular order.
Crisis on Infinite Earths (Marv Wolfman - 1985-86)
Batman: Contagion (Chuck Dixon - 1996)
X-Men: Inferno (Chris Claremont & Louise Simonson - 1988-89)
Superman: Birthright (Mark Waid - 2003-04)
Punisher: Over the Edge (Chuck Dixon - 1995)
Green Arrow: Archers Quest (Brad Meltzer - 2003)
Superman: The Man of Steel (John Byrne - 1986)
Secret Wars (Jim Shooter - 1984-85)
Secret Wars 2 (Jim Shooter - 1985-86)
Doom (Chuck Dixon - 2002)